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- PDB-8ylw: Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falcip... -

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Basic information

Entry
Database: PDB / ID: 8ylw
TitleCrystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with Lys-AMS
ComponentsLysine--tRNA ligase
KeywordsLIGASE / Malaria / LysRS / Lys-AMS / lysyladenylate analog / Inhibitor
Function / homology
Function and homology information


Transcriptional and post-translational regulation of MITF-M expression and activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSharma, V.K. / Manickam, Y. / Bagale, S. / Pradeepkumar, P.I. / Sharma, A.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 India
Department of Science & Technology (DST, India)JC Bose Fellowship Award India
CitationJournal: To Be Published
Title: Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with Lys-AMS
Authors: Sharma, V.K. / Manickam, Y. / Bagale, S. / Pradeepkumar, P.I. / Sharma, A.
History
DepositionMar 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Lysine--tRNA ligase
A: Lysine--tRNA ligase
D: Lysine--tRNA ligase
C: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,7268
Polymers234,8284
Non-polymers1,8984
Water2,882160
1
B: Lysine--tRNA ligase
A: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3634
Polymers117,4142
Non-polymers9492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10500 Å2
ΔGint-32 kcal/mol
Surface area40200 Å2
MethodPISA
2
D: Lysine--tRNA ligase
C: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3634
Polymers117,4142
Non-polymers9492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-36 kcal/mol
Surface area40310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.360, 302.190, 141.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Lysine--tRNA ligase / Lysyl-tRNA synthetase


Mass: 58706.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1350100 / Plasmid: PETM-41 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8IDJ8, lysine-tRNA ligase
#2: Chemical
ChemComp-KAA / 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / 5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE


Mass: 474.492 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H26N8O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, pH 6.5, 2% v/v Tascimate, pH 6.0 and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.5→48.11 Å / Num. obs: 89576 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 77 Å2 / CC1/2: 1 / Rrim(I) all: 0.126 / Net I/σ(I): 14.51
Reflection shellResolution: 2.5→2.65 Å / Mean I/σ(I) obs: 0.93 / Num. unique obs: 14235 / CC1/2: 0.64 / Rrim(I) all: 2.17 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.15rc1_3423-0000)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PG3

4pg3


Resolution: 2.5→45.526 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 4476 5 %
Rwork0.2091 --
obs0.212 89497 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→45.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15413 0 128 160 15701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916196
X-RAY DIFFRACTIONf_angle_d1.12921921
X-RAY DIFFRACTIONf_dihedral_angle_d4.2749782
X-RAY DIFFRACTIONf_chiral_restr0.062375
X-RAY DIFFRACTIONf_plane_restr0.0072887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.52850.39751460.39392772X-RAY DIFFRACTION100
2.5285-2.55820.3991480.38052807X-RAY DIFFRACTION100
2.5582-2.58940.39751480.35912815X-RAY DIFFRACTION100
2.5894-2.62220.41721440.34792746X-RAY DIFFRACTION100
2.6222-2.65670.39641480.33862802X-RAY DIFFRACTION100
2.6567-2.69310.46061500.36322848X-RAY DIFFRACTION100
2.6931-2.73160.37261450.35672749X-RAY DIFFRACTION100
2.7316-2.77230.39631480.33872799X-RAY DIFFRACTION100
2.7723-2.81570.4151470.30712809X-RAY DIFFRACTION100
2.8157-2.86180.35921470.28822789X-RAY DIFFRACTION100
2.8618-2.91110.31041480.26382801X-RAY DIFFRACTION100
2.9111-2.96410.31531500.24182851X-RAY DIFFRACTION100
2.9641-3.02110.31651460.2432776X-RAY DIFFRACTION100
3.0211-3.08270.32381480.24172827X-RAY DIFFRACTION100
3.0827-3.14970.30591490.24322818X-RAY DIFFRACTION100
3.1497-3.2230.33231460.24772786X-RAY DIFFRACTION100
3.223-3.30360.31581510.25042865X-RAY DIFFRACTION100
3.3036-3.39290.29941460.24152770X-RAY DIFFRACTION100
3.3929-3.49270.2861510.23122870X-RAY DIFFRACTION100
3.4927-3.60540.29411460.21852768X-RAY DIFFRACTION100
3.6054-3.73420.281520.21632877X-RAY DIFFRACTION100
3.7342-3.88360.26561470.19912801X-RAY DIFFRACTION100
3.8836-4.06020.26891510.19142863X-RAY DIFFRACTION100
4.0602-4.27410.22781510.1732876X-RAY DIFFRACTION100
4.2741-4.54170.18391500.15472845X-RAY DIFFRACTION100
4.5417-4.8920.21381500.15012862X-RAY DIFFRACTION100
4.892-5.38360.23931530.17152895X-RAY DIFFRACTION100
5.3836-6.1610.23151530.20432907X-RAY DIFFRACTION100
6.161-7.7560.29741540.20292937X-RAY DIFFRACTION100
7.756-45.5260.21691630.1853090X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -8.1758 Å / Origin y: 39.737 Å / Origin z: -51.6662 Å
111213212223313233
T0.6879 Å2-0.0557 Å2-0.0178 Å2-0.8374 Å20.0765 Å2--0.8536 Å2
L-0.0829 °2-0.0955 °20.0541 °2-0.1121 °2-0.1068 °2--1.285 °2
S-0.0225 Å °0.0317 Å °-0.0092 Å °-0.0014 Å °0.0511 Å °0.0401 Å °0.1024 Å °-0.1081 Å °0 Å °
Refinement TLS groupSelection details: all

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